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Yorodumi- PDB-1ddm: SOLUTION STRUCTURE OF THE NUMB PTB DOMAIN COMPLEXED TO A NAK PEPTIDE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ddm | ||||||
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Title | SOLUTION STRUCTURE OF THE NUMB PTB DOMAIN COMPLEXED TO A NAK PEPTIDE | ||||||
Components |
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Keywords | SIGNALING PROTEIN/TRANSFERASE / COMPLEX / SIGNAL TRANSDUCTION / PHOSPHOTYROSINE BINDING DOMAIN (PTB) / ASYMMETRIC CELL DIVISION / SIGNALING PROTEIN-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information pericardial nephrocyte differentiation / enteroendocrine cell differentiation / Malpighian tubule tip cell differentiation / regulation of nervous system development / sensory organ precursor cell fate determination / sensory organ precursor cell division / neuroblast development / muscle cell fate specification / regulation of asymmetric cell division / regulation of neuroblast proliferation ...pericardial nephrocyte differentiation / enteroendocrine cell differentiation / Malpighian tubule tip cell differentiation / regulation of nervous system development / sensory organ precursor cell fate determination / sensory organ precursor cell division / neuroblast development / muscle cell fate specification / regulation of asymmetric cell division / regulation of neuroblast proliferation / glial cell migration / negative regulation of receptor recycling / asymmetric neuroblast division / basal part of cell / embryonic heart tube development / Notch binding / centrosome localization / negative regulation of neuroblast proliferation / negative regulation of Notch signaling pathway / positive regulation of endocytosis / regulation of neurogenesis / neuroblast proliferation / protein localization / cell cortex / negative regulation of gene expression / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS USING ARIA PROTOCOLS FOR AMBIGUOUS RESTRAINTS | ||||||
Authors | Zwahlen, C. / Li, S.C. / Kay, L.E. / Pawson, T. / Forman-Kay, J.D. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Multiple modes of peptide recognition by the PTB domain of the cell fate determinant Numb. Authors: Zwahlen, C. / Li, S.C. / Kay, L.E. / Pawson, T. / Forman-Kay, J.D. #1: Journal: Nat.Struct.Biol. / Year: 1998 Title: Structure of a Numb PTB Domain-Peptide Complex Suggests a Basis for Diverse Binding Specificity Authors: Li, S.C. / Zwahlen, C. / Vincent, S.J. / McGlade, C.J. / Kay, L.E. / Pawson, T. / Forman-Kay, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ddm.cif.gz | 882.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ddm.ent.gz | 734.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ddm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1ddm ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1ddm | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15277.424 Da / Num. of mol.: 1 / Fragment: PHOSPHOTYROSINE BINDING DOMAIN (PTB) Source method: isolated from a genetically manipulated source Details: CELL FATE DETERMINANT PROTEIN / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: PGEX4T2 / Production host: Escherichia coli (E. coli) / References: UniProt: P16554 |
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#2: Protein/peptide | Mass: 1277.359 Da / Num. of mol.: 1 / Fragment: C-TERMINAL NAK 1437-1447 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: EC: 2.7.1.37 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 50mM / pH: 6 / Pressure: 1 atm / Temperature: 303 K | ||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS USING ARIA PROTOCOLS FOR AMBIGUOUS RESTRAINTS Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2088 NOE, 50 DISTANCE RETRAINTS FORM HYDROGEN BONDS, 94 CHEMICAL SHIFT-DERIVED DIHEDRAL RESTRAINTS | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY Conformers calculated total number: 150 / Conformers submitted total number: 20 |